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But Pollack is confident that when it comes to the infrastructure for the federal exchange and the data hub that will help determine what type of coverage — and subsidies — applicants can get, HHS will find the resources somehow.

“Those things are of such high priority that they will move forward,” Pollack said.

But where exactly will the money come from?

“It’s not entirely clear,” said Edwin Park, vice president of health policy at the Center on Budget and Policy Priorities. “The sequester will strain the agency’s resources,” he said, but “there is a confidence” that the crucial components will remain on track.

The administration’s budget request last year called for an additional $864 million in one-time funding to finish building the federal exchange. And HHS Secretary Kathleen Sebelius testified in budget hearings then that the $1 billion provided in the Affordable Care Act for federal implementation of the law would be spent by the end of 2012.

By contrast, the law supplied HHS with ample funding to send to states that would set up their own exchanges. California alone has received more than $910 million in exchange grants, for instance.

But HHS didn’t get another dime for its work. The continuing resolution that is funding the government through March 27 froze funding at 2012 levels. HHS is not going to get a raise and will almost certainly be targeted — successfully or not — for cuts when Congress takes up government funding again in March. Most HHS funds that can be tapped for the health law will be subject to the sequester unless it is dealt with by then.

HHS did not respond to questions about whether any of the original $1 billion for implementation remains.

Troy, the former deputy secretary of HHS, suggests one possibility for funding. He said agencies are typically allowed to move about 1 percent of their budgets around accounts as needed and that ability is not affected by the sequester. That would be about $750 million at HHS, he said.

But the political reality is that every agency constituency will be pressing HHS to use any flexibility it has in their favor, said Douglas Holtz-Eakin, former Congressional Budget Office director under Bush.

“It’s not like you could take all $750 million and stick it on Obamacare,” he said, adding that flexibility is typically diminished when applied to a controversial policy.

“I have no doubt they will use any funds they can to implement the law … but the sequester can’t be helping,” he said.